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BMC, BMC Structural Biology, 1(9), p. 27

DOI: 10.1186/1472-6807-9-27

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PTools: an opensource molecular docking library

This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

BACKGROUND: Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. RESULTS: We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. CONCLUSION: The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation.